libSBML Python API  5.10.0
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libsbml.SBMLError Class Reference
Inheritance diagram for libsbml.SBMLError:
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Detailed Description

{core}

Representation of errors, warnings and other diagnostics

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

When a libSBML operation on SBML content results in an error, or when there is something wrong with the SBML content, the problems are reported as SBMLError objects. These are generally stored in an SBMLErrorLog object; this log object, in turn, is kept in the SBMLDocument object containing the SBML content. Applications can obtain the list of logged errors using SBMLDocument.getErrorLog() and then use the methods provided by SBMLErrorLog to access individual SBMLError objects. (Note that despite the word 'error' in the name, SBMLError objects are used to represent not only 'true' errors, but also warnings and some informational diagnostics. The name is a historical hold-over from early versions of libSBML, in which the object really was only used to report errors.)

Each SBMLError object instance has an identification number that identifies the nature of the problem. This 'error id' number will be up to five digits long, and it will come from one of two sets of static integer constants defined in the interface class libsbml: either the SBML error identifiers (described below) or the XML error identifiers (described in the documentation for the class XMLError). The former set of constants includes all the SBML validation rule numbers listed in the appendices of the SBML specification documents, as well as some additional libSBML-specific error codes.

Error codes are useful mainly for software. For human readers, SBMLError also includes text messages that describe the nature of a given problem. The messages can be accessed using SBMLError.getShortMessage() and SBMLError.getMessage(). The former provides a brief one-line description of the issue, while SBMLError.getMessage() provides a more detailed text, including (if appropriate) references to sections of the SBML specifications where relevant topics are discussed. These text strings are suitable for displaying to human users.

An SBMLError object also contains a category code; its value may be retrieved using the method SBMLError.getCategory(). Category values are drawn from a set of static integer constants defined in libsbml and having names beginning with the characters LIBSBML_CAT_. The list of possible codes is described in a separate section below. Categories are used to partition errors into distinct conceptual groups. This is principally used by the libSBML validation system to group classes of validation checks. For example, LIBSBML_CAT_IDENTIFIER_CONSISTENCY is the category for tests that check identifier consistency; LIBSBML_CAT_MATHML_CONSISTENCY is the category for MathML consistency checking; and so on.

In addition, SBMLError also has a severity code. Its value may be retrieved using the method SBMLError.getSeverity(). The possible severity values are the same as those reported byXMLError. Severity levels currently range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL). They can be used by an application to evaluate how serious a given problem is.

Finally, SBMLError records the line and column near where the problem occurred in the SBML content. The values may be retrieved using the methods SBMLError.getLine() and SBMLError.getColumn(). We say 'near', because a lot of factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the SBMLError object to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Error codes associated with SBMLError objects

The error and warning codes returned by libSBML are listed in the table below. The method SBMLError.getErrorId() returns the error code of a given SBMLError object instance. In the libSBML Python language interface, these error identifiers are currently implemented as static integer constants defined in the interface class libsbml.

In this table, the right-hand columns titled 'L1V1', 'L1V2', etc. refer to Levels and Versions of the SBML specifications, and the entries in each column refer to whether the severity of the condition in that particular Level+Version of SBML. The codes stand for the following:

N= Not applicable
I= Informational
W= Warning
E= Error
F= Fatal

The text shown in the 'Meaning' is the text returned by the SBMLError.getShortMessage() method on a given SBMLError object. A longer and (hopefully) clearer explanation of the issue is returned by SBMLError.getMessage().

The error codes come from different lists depending on whether they're from libSBML core or from an SBML Level 3 package extension. However, in the language interfaces other than C++, all libSBML error codes are ultimately represented as integer constants rather than separate enumerations lists, and they are all stored in a single interface class. Codes from different libSBML extensions have names that begin with the package's nickname, such as Qual for the Qualitative Models package, Layout for the Layout package, and so on. If the name of a code does not begin with one of the package nicknames (Layout, Fbc, Comp, Qual, etc.), then it is a code from libSBML core.

Enumerator Meaning L 1 V 1 L 1 V 2 L 2 V 1 L 2 V 2 L 2 V 3 L 2 V 4 L 3 V 1
UnknownError Encountered unknown internal libSBML error F F F F F F F
NotUTF8 File does not use UTF-8 encoding E E E E E E E
UnrecognizedElement Encountered unrecognized element E E E E E E E
NotSchemaConformant Document does not conform to the SBML XML schema E E E E E E E
L3NotSchemaConformant Document is not well-formed XML N N N N N N E
InvalidMathElement Invalid MathML N N E E E E E
DisallowedMathMLSymbol Disallowed MathML symbol found N N E E E E E
DisallowedMathMLEncodingUse Use of the MathML 'encoding' attribute is not allowed on this element N N E E E E E
DisallowedDefinitionURLUse Use of the MathML 'definitionURL' attribute is not allowed on this element N N E E E E E
BadCsymbolDefinitionURLValue Invalid <csymbol> 'definitionURL' attribute value N N E E E E E
DisallowedMathTypeAttributeUse Use of the MathML 'type' attribute is not allowed on this element N N E E E E E
DisallowedMathTypeAttributeValue Disallowed MathML 'type' attribute value N N E E E E E
LambdaOnlyAllowedInFunctionDef Use of <lambda> not permitted outside of FunctionDefinition objects N N E E E E E
BooleanOpsNeedBooleanArgs Non-Boolean argument given to Boolean operator N N W E E E E
NumericOpsNeedNumericArgs Non-numerical argument given to numerical operator N N W E E E E
ArgsToEqNeedSameType Arguments to <eq> and <neq> must have the same data types N N W E E E E
PiecewiseNeedsConsistentTypes Terms in a <piecewise> expression must have consistent data types N N W E E E E
PieceNeedsBoolean The second argument of a <piece> expression must yield a Boolean value N N W E E E E
ApplyCiMustBeUserFunction A <ci> element in this context must refer to a function definition N N W E E E E
ApplyCiMustBeModelComponent A <ci> element in this context must refer to a model component N N W E E E E
KineticLawParametersAreLocalOnly Cannot use a KineticLaw local parameter outside of its local scope N N W E E E E
MathResultMustBeNumeric A formula's result in this context must be a numerical value N N W E E E E
OpsNeedCorrectNumberOfArgs Incorrect number of arguments given to MathML operator N N W E E E E
InvalidNoArgsPassedToFunctionDef Incorrect number of arguments given to function invocation N N N N N E E
DisallowedMathUnitsUse Attribute 'units' is only permitted on <cn> elements N N N N N N E
InvalidUnitsValue Invalid value given for the 'units' attribute N N N N N N E
DuplicateComponentId Duplicate 'id' attribute value E E E E E E E
DuplicateUnitDefinitionId Duplicate unit definition 'id' attribute value E E E E E E E
DuplicateLocalParameterId Duplicate local parameter 'id' attribute value E E E E E E E
MultipleAssignmentOrRateRules Multiple rules for the same variable are not allowed E E E E E E E
MultipleEventAssignmentsForId Multiple event assignments for the same variable are not allowed N N E E E E E
EventAndAssignmentRuleForId An event assignment and an assignment rule must not have the same value for 'variable' N N E E E E E
DuplicateMetaId Duplicate 'metaid' attribute value N N E E E E E
InvalidSBOTermSyntax Invalid syntax for an 'sboTerm' attribute value N N N E E E E
InvalidMetaidSyntax Invalid syntax for a 'metaid' attribute value N N E E E E E
InvalidIdSyntax Invalid syntax for an 'id' attribute value E E E E E E E
InvalidUnitIdSyntax Invalid syntax for the identifier of a unit N N N E E E E
InvalidNameSyntax Invalid syntax for a 'name' attribute value N N N N N N E
MissingAnnotationNamespace Missing declaration of the XML namespace for the annotation N N N E E E E
DuplicateAnnotationNamespaces Multiple annotations using the same XML namespace N N N E E E E
SBMLNamespaceInAnnotation The SBML XML namespace cannot be used in an Annotation object N N N E E E N
MultipleAnnotations Only one Annotation object is permitted under a given SBML object N N N N N N E
InconsistentArgUnits The units of the function call's arguments are not consistent with its definition W W W E E W W
InconsistentKineticLawUnitsL3 The kinetic law's units are inconsistent with those of other kinetic laws in the model N N N N N N W
AssignRuleCompartmentMismatch Mismatched units in assignment rule for compartment E E E E E W W
AssignRuleSpeciesMismatch Mismatched units in assignment rule for species E E E E E W W
AssignRuleParameterMismatch Mismatched units in assignment rule for parameter E E E E E W W
AssignRuleStoichiometryMismatch Mismatched units in assignment rule for stoichiometry N N N N N N W
InitAssignCompartmenMismatch Mismatched units in initial assignment to compartment N N N E E W W
InitAssignSpeciesMismatch Mismatched units in initial assignment to species N N N E E W W
InitAssignParameterMismatch Mismatched units in initial assignment to parameter N N N E E W W
InitAssignStoichiometryMismatch Mismatched units in initial assignment to stoichiometry N N N N N N W
RateRuleCompartmentMismatch Mismatched units in rate rule for compartment E E E E E W W
RateRuleSpeciesMismatch Mismatched units in rate rule for species E E E E E W W
RateRuleParameterMismatch Mismatched units in rate rule for parameter E E E E E W W
RateRuleStoichiometryMismatch Mismatched units in rate rule for stoichiometry N N N N N N W
KineticLawNotSubstancePerTime The units of the kinetic law are not 'substance'/'time' E E E E E W W
SpeciesInvalidExtentUnits The species' units are not consistent with units of extent N N N N N N W
DelayUnitsNotTime The units of the delay expression are not units of time N N E E E W W
EventAssignCompartmentMismatch Mismatched units in event assignment for compartment N N E E E W W
EventAssignSpeciesMismatch Mismatched units in event assignment for species N N E E E W W
EventAssignParameterMismatch Mismatched units in event assignment for parameter N N E E E W W
EventAssignStoichiometryMismatch Mismatched units in event assignment for stoichiometry N N N N N N W
PriorityUnitsNotDimensionless The units of a priority expression must be 'dimensionless' N N N N N N W
UpperUnitBound Upper boundary of unit validation diagnostic codes N N N N N N N
OverdeterminedSystem The model is overdetermined W W W E E E E
InvalidModelSBOTerm Invalid 'sboTerm' attribute value for a Model object N N N E E W W
InvalidFunctionDefSBOTerm Invalid 'sboTerm' attribute value for a FunctionDefinition object N N N E E W W
InvalidParameterSBOTerm Invalid 'sboTerm' attribute value for a Parameter object N N N E E W W
InvalidInitAssignSBOTerm Invalid 'sboTerm' attribute value for an InitialAssignment object N N N E E W W
InvalidRuleSBOTerm Invalid 'sboTerm' attribute value for a Rule object N N N E E W W
InvalidConstraintSBOTerm Invalid 'sboTerm' attribute value for a Constraint object N N N E E W W
InvalidReactionSBOTerm Invalid 'sboTerm' attribute value for a Reaction object N N N E E W W
InvalidSpeciesReferenceSBOTerm Invalid 'sboTerm' attribute value for a SpeciesReference object N N N E E W W
InvalidKineticLawSBOTerm Invalid 'sboTerm' attribute value for a KineticLaw object N N N E E W W
InvalidEventSBOTerm Invalid 'sboTerm' attribute value for an Event object N N N E E W W
InvalidEventAssignmentSBOTerm Invalid 'sboTerm' attribute value for an EventAssignment object N N N E E W W
InvalidCompartmentSBOTerm Invalid 'sboTerm' attribute value for a Compartment object N N N N E W W
InvalidSpeciesSBOTerm Invalid 'sboTerm' attribute value for a Species object N N N N E W W
InvalidCompartmentTypeSBOTerm Invalid 'sboTerm' attribute value for a CompartmentType object N N N N E W N
InvalidSpeciesTypeSBOTerm Invalid 'sboTerm' attribute value for a SpeciesType object N N N N E W N
InvalidTriggerSBOTerm Invalid 'sboTerm' attribute value for an Event Trigger object N N N N E W W
InvalidDelaySBOTerm Invalid 'sboTerm' attribute value for an Event Delay object N N N N E W W
NotesNotInXHTMLNamespace Notes must be placed in the XHTML XML namespace E E E E E E E
NotesContainsXMLDecl XML declarations are not permitted in Notes objects N N N E E E E
NotesContainsDOCTYPE XML DOCTYPE elements are not permitted in Notes objects N N N E E E E
InvalidNotesContent Invalid notes content found N N N E E E N
OnlyOneNotesElementAllowed Only one Notes subobject is permitted on a given SBML object N N N N N N E
InvalidNamespaceOnSBML Invalid XML namespace for the SBML container element E E E E E E E
MissingOrInconsistentLevel Missing or inconsistent value for the 'level' attribute E E E E E E E
MissingOrInconsistentVersion Missing or inconsistent value for the 'version' attribute E E E E E E E
PackageNSMustMatch Inconsistent or invalid SBML Level/Version for the package namespace declaration N N N N N N E
LevelPositiveInteger The 'level' attribute must have a positive integer value N N N N N N E
VersionPositiveInteger The 'version' attribute must have a positive integer value N N N N N N E
AllowedAttributesOnSBML Invalid attribute found on the SBML container element N N N N N N E
L3PackageOnLowerSBML An L3 package ns found on the SBML container element. W W W W W W N
MissingModel No model definition found E E E E E E E
IncorrectOrderInModel Incorrect ordering of components within the Model object E E E E E E N
EmptyListElement Empty ListOf___ object found E E E E E E E
NeedCompartmentIfHaveSpecies The presence of a species requires a compartment E E E E E E E
OneOfEachListOf Only one of each kind of ListOf___ object is allowed inside a Model object N N N N N N E
OnlyFuncDefsInListOfFuncDefs Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions N N N N N N E
OnlyUnitDefsInListOfUnitDefs Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects N N N N N N E
OnlyCompartmentsInListOfCompartments Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects N N N N N N E
OnlySpeciesInListOfSpecies Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects N N N N N N E
OnlyParametersInListOfParameters Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects N N N N N N E
OnlyInitAssignsInListOfInitAssigns Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects N N N N N N E
OnlyRulesInListOfRules Only Rule, Notes and Annotation objects are allowed in ListOfRules objects N N N N N N E
OnlyConstraintsInListOfConstraints Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects N N N N N N E
OnlyReactionsInListOfReactions Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects N N N N N N E
OnlyEventsInListOfEvents Only Event, Notes and Annotation objects are allowed in ListOfEvents objects N N N N N N E
L3ConversionFactorOnModel A 'conversionFactor' attribute value must reference a Parameter object N N N N N N E
L3TimeUnitsOnModel Invalid 'timeUnits' attribute value N N N N N N W
L3VolumeUnitsOnModel Invalid 'volumeUnits' attribute value N N N N N N W
L3AreaUnitsOnModel Invalid 'areaUnits' attribute value N N N N N N W
L3LengthUnitsOnModel Invalid 'lengthUnits' attribute value N N N N N N W
L3ExtentUnitsOnModel Invalid 'extentUnits' attribute value N N N N N N W
AllowedAttributesOnModel Invalid attribute found on the Model object N N N N N N E
AllowedAttributesOnListOfFuncs Invalid attribute found on the ListOfFunctionDefinitions object N N N N N N E
AllowedAttributesOnListOfUnitDefs Invalid attribute found on the ListOfUnitDefinitions object N N N N N N E
AllowedAttributesOnListOfComps Invalid attribute found on the ListOfCompartments object N N N N N N E
AllowedAttributesOnListOfSpecies Invalid attribute found on the ListOfSpecies object N N N N N N E
AllowedAttributesOnListOfParams Invalid attribute found on the ListOfParameters object N N N N N N E
AllowedAttributesOnListOfInitAssign Invalid attribute found on the ListOfInitialAssignments object N N N N N N E
AllowedAttributesOnListOfRules Invalid attribute found on the ListOfRules object N N N N N N E
AllowedAttributesOnListOfConstraints Invalid attribute found on the ListOfConstraints object N N N N N N E
AllowedAttributesOnListOfReactions Invalid attribute found on the ListOfReactions object N N N N N N E
AllowedAttributesOnListOfEvents Invalid attribute found on the ListOfEvents object N N N N N N E
FunctionDefMathNotLambda Invalid expression found in the function definition N N E E E E E
InvalidApplyCiInLambda Invalid forward reference in the MathML <apply><ci>...</ci></apply> expression N N E E E N N
RecursiveFunctionDefinition Recursive function definitions are not permitted N N E E E E E
InvalidCiInLambda Invalid <ci> reference found inside the <lambda> mathematical formula N N E E E E E
InvalidFunctionDefReturnType A function's return type must be either a number or a Boolean N N E E E E E
OneMathElementPerFunc A FunctionDefinition object must contain one <math> element N N N N N N E
AllowedAttributesOnFunc Invalid attribute found on the FunctionDefinition object N N N N N N E
InvalidUnitDefId Invalid 'id' attribute value for a UnitDefinition object E E E E E E E
InvalidSubstanceRedefinition Invalid redefinition of built-in type 'substance' E E E E E E N
InvalidLengthRedefinition Invalid redefinition of built-in type 'length' W W E E E E N
InvalidAreaRedefinition Invalid redefinition of built-in type name 'area' W W E E E E N
InvalidTimeRedefinition Invalid redefinition of built-in type name 'time' E E E E E E N
InvalidVolumeRedefinition Invalid redefinition of built-in type name 'volume' E E E E E E N
VolumeLitreDefExponentNotOne Must use 'exponent'=1 when defining 'volume' in terms of litres E E E E E N N
VolumeMetreDefExponentNot3 Must use 'exponent'=3 when defining 'volume' in terms of metres N N E E E N N
EmptyListOfUnits An empty list of Unit objects is not permitted in a UnitDefinition object E E E E E E N
InvalidUnitKind Invalid value for the 'kind' attribute of a UnitDefinition object E E E E E E E
OffsetNoLongerValid Unit attribute 'offset' is not supported in this Level+Version of SBML N N N E E E N
CelsiusNoLongerValid Unit name 'Celsius' is not defined in this Level+Version of SBML N N N E E E N
EmptyUnitListElement A ListOfUnits object must not be empty N N N N N N E
OneListOfUnitsPerUnitDef At most one ListOfUnits object is allowed inside a UnitDefinition object N N N N N N E
OnlyUnitsInListOfUnits Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects N N N N N N E
AllowedAttributesOnUnitDefinition Invalid attribute found on the UnitDefinition object N N N N N N E
AllowedAttributesOnListOfUnits Invalid attribute found on the ListOfUnits object N N N N N N E
AllowedAttributesOnUnit Invalid attribute found on the Unit object N N N N N N E
ZeroDimensionalCompartmentSize Invalid use of the 'size' attribute for a zero-dimensional compartment N N E E E E N
ZeroDimensionalCompartmentUnits Invalid use of the 'units' attribute for a zero-dimensional compartment N N E E E E N
ZeroDimensionalCompartmentConst Zero-dimensional compartments must be defined to be constant N N E E E E N
UndefinedOutsideCompartment Invalid value for the 'outside' attribute of a Compartment object E E E E E E N
RecursiveCompartmentContainment Recursive nesting of compartments via the 'outside' attribute is not permitted W W W E E E N
ZeroDCompartmentContainment Invalid nesting of zero-dimensional compartments N N W E E E N
Invalid1DCompartmentUnits Invalid value for the 'units' attribute of a one-dimensional compartment N N E E E E W
Invalid2DCompartmentUnits Invalid value for the 'units' attribute of a two-dimensional compartment N N E E E E W
Invalid3DCompartmentUnits Invalid value for the 'units' attribute of a three-dimensional compartment E E E E E E W
InvalidCompartmentTypeRef Invalid value for the 'compartmentType' attribute of a compartment N N N E E E N
OneDimensionalCompartmentUnits No units defined for 1-D compartment N N N N N N W
TwoDimensionalCompartmentUnits No units defined for 2-D compartment N N N N N N W
ThreeDimensionalCompartmentUnits No units defined for 3-D Compartment object N N N N N N W
AllowedAttributesOnCompartment Invalid attribute found on Compartment object N N N N N N E
NoUnitsOnCompartment No units defined for Compartment object N N N N N N W
InvalidSpeciesCompartmentRef Invalid value found for Species 'compartment' attribute E E E E E E E
HasOnlySubsNoSpatialUnits Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true' N N E E N N N
NoSpatialUnitsInZeroD Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional N N E E N N N
NoConcentrationInZeroD Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional N N E E E E N
SpatialUnitsInOneD Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment N N E E N N N
SpatialUnitsInTwoD Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment N N E E N N N
SpatialUnitsInThreeD Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment N N E E N N N
InvalidSpeciesSusbstanceUnits Invalid value for a Species 'units' attribute E E E E E E W
BothAmountAndConcentrationSet Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously N N E E E E E
NonBoundarySpeciesAssignedAndUsed Cannot use a non-boundary species in both reactions and rules simultaneously W W E E E E E
NonConstantSpeciesUsed Cannot use a constant, non-boundary species as a reactant or product N N E E E E E
InvalidSpeciesTypeRef Invalid value for the 'speciesType' attribute of a species N N N E E E N
MultSpeciesSameTypeInCompartment Cannot have multiple species of the same species type in the same compartment N N N E E E N
MissingSpeciesCompartment Missing value for the 'compartment' attribute E E E E E E E
SpatialSizeUnitsRemoved Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML N N N N E E N
SubstanceUnitsOnSpecies No substance units defined for the species N N N N N N W
ConversionFactorOnSpecies Invalid value for the 'conversionFactor' attribute N N N N N N E
AllowedAttributesOnSpecies Invalid attribute found on Species object N N N N N N E
InvalidParameterUnits Invalid value for the 'units' attribute of a Parameter object E E E E E E W
ParameterUnits No units defined for the parameter N N N N N N W
ConversionFactorMustConstant A conversion factor must reference a Parameter object declared to be a constant N N N N N N E
AllowedAttributesOnParameter Invalid attribute found on Parameter object N N N N N N E
InvalidInitAssignSymbol Invalid value for the 'symbol' attribute of an InitialAssignment object N N N E E E E
MultipleInitAssignments Multiple initial assignments for the same 'symbol' value are not allowed N N N E E E E
InitAssignmentAndRuleForSameId Cannot set a value using both an initial assignment and an assignment rule simultaneously N N N E E E E
OneMathElementPerInitialAssign An InitialAssignment object must contain one <math> element N N N N N N E
AllowedAttributesOnInitialAssign Invalid attribute found on an InitialAssignment object N N N N N N E
InvalidAssignRuleVariable Invalid value for the 'variable' attribute of an AssignmentRule object E E E E E E E
InvalidRateRuleVariable Invalid value for the 'variable' attribute of a RateRule object E E E E E E E
AssignmentToConstantEntity An assignment rule cannot assign an entity declared to be constant N N E E E E E
RateRuleForConstantEntity A rate rule cannot assign an entity declared to be constant N N E E E E E
CircularRuleDependency Circular dependencies involving rules and reactions are not permitted N N N E E E E
OneMathElementPerRule A rule object must contain one <math> element N N N N N N E
AllowedAttributesOnAssignRule Invalid attribute found on an AssignmentRule object N N N N N N E
AllowedAttributesOnRateRule Invalid attribute found on a RateRule object N N N N N N E
AllowedAttributesOnAlgRule Invalid attribute found on an AlgebraicRule object N N N N N N E
ConstraintMathNotBoolean A Constraint object's <math> must evaluate to a Boolean value N N N E E E E
IncorrectOrderInConstraint Subobjects inside the Constraint object are not in the prescribed order N N N E E E N
ConstraintNotInXHTMLNamespace A Constraint's Message subobject must be in the XHTML XML namespace N N N E E E N
ConstraintContainsXMLDecl XML declarations are not permitted within Constraint's Message objects N N N E E E E
ConstraintContainsDOCTYPE XML DOCTYPE elements are not permitted within Constraint's Message objects N N N E E E E
InvalidConstraintContent Invalid content for a Constraint object's Message object N N N E E E N
OneMathElementPerConstraint A Constraint object must contain one <math> element N N N N N N E
OneMessageElementPerConstraint A Constraint object must contain one Message subobject N N N N N N E
AllowedAttributesOnConstraint Invalid attribute found on Constraint object N N N N N N E
NoReactantsOrProducts Cannot have a reaction with neither reactants nor products E E E E E E E
IncorrectOrderInReaction Subobjects inside the Reaction object are not in the prescribed order E E E E E E N
EmptyListInReaction Reaction components, if present, cannot be empty E E E E E E E
InvalidReactantsProductsList Invalid object found in the list of reactants or products E E E E E E E
InvalidModifiersList Invalid object found in the list of modifiers N N E E E E E
OneSubElementPerReaction A Reaction object can only contain one of each allowed type of object N N N N N N E
CompartmentOnReaction Invalid value for the Reaction 'compartment' attribute N N N N N N E
AllowedAttributesOnReaction Invalid attribute for a Reaction object N N N N N N E
InvalidSpeciesReference Invalid 'species' attribute value in SpeciesReference object E E E E E E E
BothStoichiometryAndMath The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive N N E E E E N
AllowedAttributesOnSpeciesReference Invalid attribute found on the SpeciesReference object N N N N N N E
AllowedAttributesOnModifier Invalid attribute found on the ModifierSpeciesReference object N N N N N N E
UndeclaredSpeciesRef Unknown species referenced in the kinetic law <math> formula W W E E E E E
IncorrectOrderInKineticLaw Incorrect ordering of components in the KineticLaw object N N E E E E N
EmptyListInKineticLaw The list of parameters, if present, cannot be empty E E E E E E E
NonConstantLocalParameter Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true' N N W E E E N
SubsUnitsNoLongerValid Attribute 'substanceUnits' is not supported in this Level+Version of SBML N N N E E E N
TimeUnitsNoLongerValid Attribute 'timeUnits' is not supported in this Level+Version of SBML N N N E E E N
OneListOfPerKineticLaw Only one ListOfLocalParameters object is permitted within a KineticLaw object N N N N N N E
OnlyLocalParamsInListOfLocalParams Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects N N N N N N E
AllowedAttributesOnListOfLocalParam Invalid attribute found on the ListOfLocalParameters object N N N N N N E
OneMathPerKineticLaw Only one <math> element is allowed in a KineticLaw object N N E E E E E
UndeclaredSpeciesInStoichMath Unknown species referenced in the StoichiometryMath object's <math> formula N N W E E E N
AllowedAttributesOnKineticLaw Invalid attribute found on the KineticLaw object N N N N N N E
AllowedAttributesOnListOfSpeciesRef Invalid attribute found on the ListOfSpeciesReferences object N N N N N N E
AllowedAttributesOnListOfMods Invalid attribute found on the ListOfModifiers object N N N N N N E
AllowedAttributesOnLocalParameter Invalid attribute found on the LocalParameter object N N N N N N E
MissingTriggerInEvent The Event object is missing a Trigger subobject N N E E E E E
TriggerMathNotBoolean A Trigger object's <math> expression must evaluate to a Boolean value N N E E E E E
MissingEventAssignment The Event object is missing an EventAssignment subobject N N E E E E E
TimeUnitsEvent Units referenced by 'timeUnits' attribute are not compatible with units of time N N E E N N N
IncorrectOrderInEvent Incorrect ordering of components in Event object N N E E E E N
ValuesFromTriggerTimeNeedDelay Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay N N N N N E N
DelayNeedsValuesFromTriggerTime The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime' N N N N N N N
OneMathPerTrigger A Trigger object must have one <math> element N N N N N N E
OneMathPerDelay A Delay object must have one <math> element N N N N N N E
InvalidEventAssignmentVariable Invalid 'variable' attribute value in Event object N N E E E E E
EventAssignmentForConstantEntity An EventAssignment object cannot assign to a component having attribute 'constant'='true' N N W E E E E
OneMathPerEventAssignment An EventAssignment object must have one <math> element N N N N N N E
AllowedAttributesOnEventAssignment Invalid attribute found on the EventAssignment object N N N N N N E
OnlyOneDelayPerEvent An Event object can only have one Delay subobject N N N N N N E
OneListOfEventAssignmentsPerEvent An Event object can only have one ListOfEventAssignments subobject N N N N N N E
OnlyEventAssignInListOfEventAssign Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments N N N N N N E
AllowedAttributesOnListOfEventAssign Invalid attribute found on the ListOfEventAssignments object N N N N N N E
AllowedAttributesOnEvent Invalid attribute found on the Event object N N N N N N E
AllowedAttributesOnTrigger Invalid attribute found on the Trigger object N N N N N N E
AllowedAttributesOnDelay Invalid attribute found on the Delay object N N N N N N E
PersistentNotBoolean The Trigger attribute 'persistent' must evaluate to a Boolean value N N N N N N E
InitialValueNotBoolean The Trigger attribute 'initialValue' must evaluate to a Boolean value N N N N N N E
OnlyOnePriorityPerEvent An Event object can only have one Priority subobject N N N N N N E
OneMathPerPriority A Priority object must have one <math> element N N N N N N E
AllowedAttributesOnPriority Invalid attribute found on the Priority object N N N N N N E
GeneralWarningNotSpecified Unknown error N N N N N N N
CompartmentShouldHaveSize It's best to define a size for every compartment in a model N N W W W W W
SpeciesShouldHaveValue It's best to define an initial amount or initial concentration for every species in a model N N W W W W W
ParameterShouldHaveUnits It's best to declare units for every parameter in a model W W W W W W W
LocalParameterShadowsId Local parameters defined within a kinetic law shadow global object symbols W W W W W W W
CannotConvertToL1V1 Cannot convert to SBML Level 1 Version 1 N E E E E E E
NoEventsInL1 SBML Level 1 does not support events N N E E E E E
NoFunctionDefinitionsInL1 SBML Level 1 does not support function definitions N N W W W W W
NoConstraintsInL1 SBML Level 1 does not support constraints N N N W W W W
NoInitialAssignmentsInL1 SBML Level 1 does not support initial assignments N N N W W W W
NoSpeciesTypesInL1 SBML Level 1 does not support species types N N N W W W N
NoCompartmentTypeInL1 SBML Level 1 does not support compartment types N N N W W W N
NoNon3DCompartmentsInL1 SBML Level 1 only supports three-dimensional compartments N N E E E E E
NoFancyStoichiometryMathInL1 SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas N N E E E E E
NoNonIntegerStoichiometryInL1 SBML Level 1 does not support non-integer 'stoichiometry' attribute values N N E E E E E
NoUnitMultipliersOrOffsetsInL1 SBML Level 1 does not support multipliers or offsets in unit definitions N N E E E E E
SpeciesCompartmentRequiredInL1 In SBML Level 1, a value for 'compartment' is mandatory in species definitions N N E E E E E
NoSpeciesSpatialSizeUnitsInL1 SBML Level 1 does not support species 'spatialSizeUnits' settings N N E E E E N
NoSBOTermsInL1 SBML Level 1 does not support the 'sboTerm' attribute N N N W W W W
StrictUnitsRequiredInL1 SBML Level 1 requires strict unit consistency N N N N N W W
ConversionFactorNotInL1 SBML Level 1 does not support the 'conversionFactor' attribute N N N N N N E
CompartmentNotOnL1Reaction SBML Level 1 does not support the 'compartment' attribute on Reaction objects N N N N N N W
ExtentUnitsNotSubstance Units of extent must be compatible with units of substance N N N N N N E
GlobalUnitsNotDeclared Global units must be refer to unit kind or unitDefinition. N N N N N N E
HasOnlySubstanceUnitsNotinL1 The concept of hasOnlySubstanceUnits was not available in SBML Level 1. N N E E E E E
AvogadroNotSupported Avogadro not supported in Levels 2 and 1. N N N N N N E
NoConstraintsInL2v1 SBML Level 2 Version 1 does not support Constraint objects N N N W W W W
NoInitialAssignmentsInL2v1 SBML Level 2 Version 1 does not support InitialAssignment objects N N N W W W W
NoSpeciesTypeInL2v1 SBML Level 2 Version 1 does not support SpeciesType objects N N N W W W N
NoCompartmentTypeInL2v1 SBML Level 2 Version 1 does not support CompartmentType objects N N N W W W N
NoSBOTermsInL2v1 SBML Level 2 Version 1 does not support the 'sboTerm' attribute N N N W W W W
NoIdOnSpeciesReferenceInL2v1 SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects N N N W W W W
NoDelayedEventAssignmentInL2v1 SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute N N N N N E E
StrictUnitsRequiredInL2v1 SBML Level 2 Version 1 requires strict unit consistency N N N N N W W
IntegerSpatialDimensions SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3 N N N N N N E
StoichiometryMathNotYetSupported Conversion to StoichiometryMath objects not yet supported N N N N N N N
PriorityLostFromL3 SBML Level 2 Version 1 does not support priorities on Event objects N N N N N N E
NonPersistentNotSupported SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects N N N N N N E
InitialValueFalseEventNotSupported SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects N N N N N N E
SBOTermNotUniversalInL2v2 The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2 N N N N W W W
NoUnitOffsetInL2v2 This Level+Version of SBML does not support the 'offset' attribute on Unit objects N N E N N N N
NoKineticLawTimeUnitsInL2v2 This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects E E E N N N N
NoKineticLawSubstanceUnitsInL2v2 This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects E E E N N N N
NoDelayedEventAssignmentInL2v2 This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute N N N N N E E
ModelSBOBranchChangedBeyondL2v2 The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version N N N N N E E
StrictUnitsRequiredInL2v2 SBML Level 2 Version 2 requires strict unit consistency N N N N N W W
StrictSBORequiredInL2v2 SBML Level 2 Version 2 requires strict SBO term consistency N N N N N W W
DuplicateAnnotationInvalidInL2v2 Duplicate top-level annotations are invalid in SBML Level 2 Version 2 W W W N N N N
NoUnitOffsetInL2v3 This Level+Version of SBML does not support the 'offset' attribute on Unit objects N N E N N N N
NoKineticLawTimeUnitsInL2v3 This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects E E E N N N N
NoKineticLawSubstanceUnitsInL2v3 This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects E E E N N N N
NoSpeciesSpatialSizeUnitsInL2v3 This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects N N E E N N N
NoEventTimeUnitsInL2v3 This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects N N E E N N N
NoDelayedEventAssignmentInL2v3 This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute N N N N N E E
ModelSBOBranchChangedBeyondL2v3 The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version N N N N N E E
StrictUnitsRequiredInL2v3 SBML Level 2 Version 3 requires strict unit consistency N N N N N W W
StrictSBORequiredInL2v3 SBML Level 2 Version 3 requires strict SBO term consistency N N N N N W W
DuplicateAnnotationInvalidInL2v3 Duplicate top-level annotations are invalid in SBML Level 2 Version 3 W W W N N N N
NoUnitOffsetInL2v4 This Level+Version of SBML does not support the 'offset' attribute on Unit objects N N E N N N N
NoKineticLawTimeUnitsInL2v4 This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects E E E N N N N
NoKineticLawSubstanceUnitsInL2v4 This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects E E E N N N N
NoSpeciesSpatialSizeUnitsInL2v4 This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects N N E E N N N
NoEventTimeUnitsInL2v4 This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects N N E E N N N
ModelSBOBranchChangedInL2v4 The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version N N N E E N N
DuplicateAnnotationInvalidInL2v4 Duplicate top-level annotations are invalid in SBML Level 2 Version 4 W W W N N N N
NoSpeciesTypeInL3v1 SBML Level 3 Version 1 does not support SpeciesType objects N N N W W W N
NoCompartmentTypeInL3v1 SBML Level 3 Version 1 does not support CompartmentType objects N N N W W W N
NoUnitOffsetInL3v1 This Level+Version of SBML does not support the 'offset' attribute on Unit objects N N E N N N N
NoKineticLawTimeUnitsInL3v1 This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects E E E N N N N
NoKineticLawSubstanceUnitsInL3v1 This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects E E E N N N N
NoSpeciesSpatialSizeUnitsInL3v1 This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects N N E E N N N
NoEventTimeUnitsInL3v1 This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects N N E E N N N
ModelSBOBranchChangedInL3v1 The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version N N N E E N N
DuplicateAnnotationInvalidInL3v1 Duplicate top-level annotations are invalid in SBML Level 3 Version 1 W W W N N N N
NoCompartmentOutsideInL3v1 This Level+Version of SBML does not support the 'outside' attribute on Compartment objects W W W W W W N
NoStoichiometryMathInL3v1 This Level+Version of SBML does not support the StoichiometryMath object N N E E E E N
InvalidSBMLLevelVersion Unknown Level+Version combination of SBML E E E E E E E
AnnotationNotesNotAllowedLevel1 Annotation objects on the SBML container element are not permitted in SBML Level 1 E E N N N N N
InvalidRuleOrdering Invalid ordering of rules E E E N N N N
RequiredPackagePresent The SBML document requires an SBML Level 3 package unavailable in this software N N N N N N E
UnrequiredPackagePresent The SBML document uses an SBML Level 3 package unavailable in this software N N N N N N W
PackageRequiredShouldBeFalse This package expects required to be false. N N N N N N W
SubsUnitsAllowedInKL Disallowed value for attribute 'substanceUnits' on KineticLaw object E E E N N N N
TimeUnitsAllowedInKL Disallowed value for attribute 'timeUnits' on KineticLaw object E E E N N N N
FormulaInLevel1KL Only predefined functions are allowed in SBML Level 1 formulas E E N N N N N
L3SubstanceUnitsOnModel Invalid 'substanceUnits' attribute value N N N N N N W
TimeUnitsRemoved This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects N N N N E E E
BadMathML Invalid MathML expression N N E E E E E
FailedMathMLReadOfDouble Missing or invalid floating-point number in MathML expression N N E E E E E
FailedMathMLReadOfInteger Missing or invalid integer in MathML expression N N E E E E E
FailedMathMLReadOfExponential Missing or invalid exponential expression in MathML N N E E E E E
FailedMathMLReadOfRational Missing or invalid rational expression in MathML N N E E E E E
BadMathMLNodeType Invalid MathML element N N E E E E E
NoTimeSymbolInFunctionDef Use of <csymbol> for 'time' not allowed within FunctionDefinition objects N N W E E E E
NoBodyInFunctionDef There must be a <lambda> body within the <math> element of a FunctionDefinition object N N E E E E E
DanglingUnitSIdRef Units must refer to valid unit or unitDefinition W W W W W W W
RDFMissingAboutTag RDF missing the <about> tag. N N N W W W W
RDFEmptyAboutTag RDF empty <about> tag. N N N W W W W
RDFAboutTagNotMetaid RDF <about> tag is not metaid. N N N W W W W
RDFNotCompleteModelHistory RDF does not contain valid ModelHistory. N N N W W W W
RDFNotModelHistory RDF does not result in a ModelHistory. N N N W W W W
AnnotationNotElement Annotation must contain element. N N N W W W W
UndeclaredUnits Missing unit declarations on parameters or literal numbers in expression W W W W W W W
UndeclaredTimeUnitsL3 Unable to verify consistency of units: the unit of time has not been declared N N N N N N W
UndeclaredExtentUnitsL3 Unable to verify consistency of units: the units of reaction extent have not been declared N N N N N N W
UndeclaredObjectUnitsL3 Unable to verify consistency of units: encountered a model entity with no declared units N N N N N N W
UnrecognisedSBOTerm Unrecognized 'sboTerm' attribute value N N N W W W W
ObseleteSBOTerm Obsolete 'sboTerm' attribute value N N N W W W W
IncorrectCompartmentSpatialDimensions In SBML Level 1, only three-dimensional compartments are allowed E E N N N N N
CompartmentTypeNotValidAttribute CompartmentType objects are not available in this Level+Version of SBML E E E N N N E
ConstantNotValidAttribute This Level+Version of SBML does not support the 'constant' attribute on this component E E N N N N N
MetaIdNotValidAttribute Attribute 'metaid' is not available in SBML Level 1 E E N N N N N
SBOTermNotValidAttributeBeforeL2V3 The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3 E E E E N N N
InvalidL1CompartmentUnits Invalid units for a compartment in SBML Level 1 E E N N N N N
L1V1CompartmentVolumeReqd In SBML Level 1, a compartment's volume must be specified E N N N N N N
CompartmentTypeNotValidComponent CompartmentType objects are not available in this Level+Version of SBML E E E N N N E
ConstraintNotValidComponent Constraint objects are not available in this Level+Version of SBML E E E N N N N
EventNotValidComponent Event objects are not available in this Level+Version of SBML E E N N N N N
SBOTermNotValidAttributeBeforeL2V2 The 'sboTerm' attribute is invalid for this component before Level 2 Version 2 E E E N N N N
FuncDefNotValidComponent FunctionDefinition objects are not available in this Level+Version of SBML E E N N N N N
InitialAssignNotValidComponent InitialAssignment objects are not available in this Level+Version of SBML E E E N N N N
VariableNotValidAttribute Attribute 'variable' is not available on this component in this Level+Version of SBML E E E E E E E
UnitsNotValidAttribute Attribute 'units' is not available on this component in this Level+Version of SBML E E E E E E E
ConstantSpeciesNotValidAttribute Attribute 'constant' is not available on Species objects in SBML Level 1 E E N N N N N
SpatialSizeUnitsNotValidAttribute Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1 E E N N N N N
SpeciesTypeNotValidAttribute Attribute 'speciesType' is not available on Species objects in SBML Level 1 E E E N N N E
HasOnlySubsUnitsNotValidAttribute Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1 E E N N N N N
IdNotValidAttribute Attribute 'id' is not available on SpeciesReference objects in SBML Level 1 E E E N N N N
NameNotValidAttribute Attribute 'name' is not available on SpeciesReference objects in SBML Level 1 E E E N N N N
SpeciesTypeNotValidComponent The SpeciesType object is not supported in SBML Level 1 E E E N N N E
StoichiometryMathNotValidComponent The StoichiometryMath object is not supported in SBML Level 1 E E N N N N E
MultiplierNotValidAttribute Attribute 'multiplier' on Unit objects is not supported in SBML Level 1 E E N N N N N
OffsetNotValidAttribute Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1 E E N N N N N
L3SpatialDimensionsUnset No value given for 'spatialDimensions' attribute; assuming a value of 3 N N N N N N W
PackageConversionNotSupported Conversion of SBML Level 3 package constructs is not yet supported E E E E E E E
InvalidTargetLevelVersion The requested SBML Level/Version combination is not known to exist E E E E E E E
L3NotSupported SBML Level 3 is not yet supported E E E E E E E
CompUnknown Unknown error from comp N N N N N N E
CompNSUndeclared The comp ns is not correctly declared N N N N N N E
CompElementNotInNs Element not in comp namespace N N N N N N E
CompDuplicateComponentId Duplicate 'id' attribute value N N N N N N E
CompUniqueModelIds Model and ExternalModelDefinitions must have unique ids N N N N N N E
CompUniquePortIds Ports must have unique ids N N N N N N E
CompInvalidSIdSyntax Invalid SId syntax N N N N N N E
CompInvalidSubmodelRefSyntax Invalid submodelRef syntax N N N N N N E
CompInvalidDeletionSyntax Invalid deletion syntax N N N N N N E
CompInvalidConversionFactorSyntax Invalid conversionFactor syntax N N N N N N E
CompInvalidNameSyntax Invalid name syntax N N N N N N E
CompReplacedUnitsShouldMatch Units of replaced elements should match replacement units. N N N N N N W
CompOneListOfReplacedElements Only one <listOfReplacedElements> allowed. N N N N N N E
CompLOReplaceElementsAllowedElements Allowed children of <listOfReplacedElements> N N N N N N E
CompLOReplacedElementsAllowedAttribs Allowed <listOfReplacedElements> attributes N N N N N N E
CompEmptyLOReplacedElements <listOfReplacedElements> must not be empty N N N N N N E
CompOneReplacedByElement Only one <replacedBy> object allowed. N N N N N N E
CompAttributeRequiredMissing Required comp:required attribute on <sbml> N N N N N N E
CompAttributeRequiredMustBeBoolean The comp:required attribute must be Boolean N N N N N N E
CompRequiredTrueIfElementsRemain The comp:required attribute must be 'true' if math changes. NOTE: Deprecated N N N N N N E
CompRequiredFalseIfAllElementsReplaced The comp:required attribute must be 'false' if math does not change. NOTE: Deprecated N N N N N N E
CompOneListOfModelDefinitions Only one <listOfModelDefinitions> allowed. N N N N N N E
CompEmptyLOModelDefs <listOfModelDefinitions> and <listOfExternalModelDefinitions> must not be empty N N N N N N E
CompLOModelDefsAllowedElements Only <modelDefinitions> in <listOfModelDefinitions> N N N N N N E
CompLOExtModelDefsAllowedElements Only <externalModelDefinitions> in <listOfExternalModelDefinitions> N N N N N N E
CompLOModelDefsAllowedAttributes Allowed <listOfModelDefinitions> attributes N N N N N N E
CompLOExtModDefsAllowedAttributes Allowed <listOfExternalModelDefinitions> attributes N N N N N N E
CompOneListOfExtModelDefinitions Only one <listOfExternalModelDefinitions> allowed. N N N N N N E
CompAttributeRequiredMustBeTrue The comp:required attribute must be 'true' N N N N N N E
CompExtModDefAllowedCoreAttributes Allowed <externalModelDefinitions> core attributes N N N N N N E
CompExtModDefAllowedElements Allowed <externalModelDefinitions> elements N N N N N N E
CompExtModDefAllowedAttributes Allowed <externalModelDefinitions> attributes N N N N N N E
CompReferenceMustBeL3 External models must be L3 N N N N N N E
CompModReferenceMustIdOfModel 'modelRef' must be the 'id' of a model in the 'source' document N N N N N N E
CompExtModMd5DoesNotMatch MD5 checksum does not match the 'source' document N N N N N N W
CompInvalidSourceSyntax The 'comp:source' attribute must be of type 'anyURI' N N N N N N E
CompInvalidModelRefSyntax The 'comp:modelRef' attribute must have the syntax of 'SId' N N N N N N E
CompInvalidMD5Syntax The 'comp:md5' attribute must have the syntax of 'string' N N N N N N E
CompCircularExternalModelReference Circular reference in <externalModelDefinitiongt; N N N N N N E
CompOneListOfOnModel Only one <listOfSubmodels> and one <listOfPorts> allowed N N N N N N E
CompNoEmptyListOfOnModel No empty listOf elements allowed N N N N N N E
CompLOSubmodelsAllowedElements Allowed elements on <listOfSubmodels> N N N N N N E
CompLOPortsAllowedElements Allowed elements on <listOfPorts> N N N N N N E
CompLOSubmodelsAllowedAttributes Allowed attributes on <listOfSubmodels> N N N N N N E
CompLOPortsAllowedAttributes Allowed attributes on <listOfPorts> N N N N N N E
CompSubmodelAllowedCoreAttributes Allowed core attributes on <submodel> N N N N N N E
CompSubmodelAllowedElements Allowed elements on <submodel> N N N N N N E
CompOneListOfDeletionOnSubmodel Only one <listOfDeletions> on a <submodel> allowed N N N N N N E
CompSubmodelNoEmptyLODeletions No empty listOfDeletions elements allowed N N N N N N E
CompLODeletionsAllowedElements Allowed elements on <listOfDeletions> N N N N N N E
CompLODeletionAllowedAttributes Allowed <listOfDeletions> attributes N N N N N N E
CompSubmodelAllowedAttributes Allowed <submodel> attributes N N N N N N E
CompModReferenceSyntax 'comp:modelRef' must conform to SId syntax N N N N N N E
CompInvalidTimeConvFactorSyntax 'comp:timeConversionFactor' must conform to SId syntax N N N N N N E
CompInvalidExtentConvFactorSyntax 'comp:extentConversionFactor' must conform to SId syntax N N N N N N E
CompSubmodelMustReferenceModel The 'comp:modelRef' attribute must reference a model N N N N N N E
CompSubmodelCannotReferenceSelf The 'comp:modelRef' attribute cannot reference own model N N N N N N E
CompModCannotCircularlyReferenceSelf <model> may not reference <submodel> that references itself. N N N N N N E
CompTimeConversionMustBeParameter The 'comp:timeConversionFactor' must reference a parameter N N N N N N E
CompExtentConversionMustBeParameter The 'comp:extentConversionFactor' must reference a parameter N N N N N N E
CompPortRefMustReferencePort The 'comp:portRef' attribute must be the 'id' of a <port> N N N N N N E
CompIdRefMustReferenceObject The 'comp:idRef' attribute must be the 'id' of a model element N N N N N N E
CompUnitRefMustReferenceUnitDef The 'comp:unitRef' attribute must be the 'id' of a UnitDefinition N N N N N N E
CompMetaIdRefMustReferenceObject The 'comp:metaIdRef' attribute must be the 'metaid' of an object N N N N N N E
CompParentOfSBRefChildMustBeSubmodel If <sBaseRef> has a child <sBaseRef> its parent must be a <submodel> N N N N N N E
CompInvalidPortRefSyntax The 'comp:portRef' attribute must have the syntax of an SBML SId N N N N N N E
CompInvalidIdRefSyntax The 'comp:idRef' attribute must have the syntax of an SBML SId N N N N N N E
CompInvalidUnitRefSyntax The 'comp:unitRef' attribute must have the syntax of an SBML SId N N N N N N E
CompInvalidMetaIdRefSyntax The 'comp:metaIdRef' attribute must have the syntax of an XML ID N N N N N N E
CompOneSBaseRefOnly Only one <sbaseRef> N N N N N N E
CompDeprecatedSBaseRefSpelling The spelling 'sbaseRef' is deprecated N N N N N N W
CompSBaseRefMustReferenceObject An SBaseRef must reference an object. N N N N N N E
CompSBaseRefMustReferenceOnlyOneObject An SBaseRef must reference only one other object. N N N N N N E
CompNoMultipleReferences Objects may not be referenced by multiple SBaseRef constructs. N N N N N N E
CompPortMustReferenceObject Port must reference an object N N N N N N E
CompPortMustReferenceOnlyOneObject Port must reference only one other object. N N N N N N E
CompPortAllowedAttributes Allowed attributes on a Port N N N N N N E
CompPortReferencesUnique Port definitions must be unique. N N N N N N E
CompDeletionMustReferenceObject Deletion must reference an object N N N N N N E
CompDeletionMustReferOnlyOneObject Deletion must reference only one other object. N N N N N N E
CompDeletionAllowedAttributes Allowed attributes on a Deletion N N N N N N E
CompReplacedElementMustRefObject ReplacedElement must reference an object N N N N N N E
CompReplacedElementMustRefOnlyOne ReplacedElement must reference only one other object. N N N N N N E
CompReplacedElementAllowedAttributes Allowed attributes on <replacedElement> N N N N N N E
CompReplacedElementSubModelRef The 'comp:submodelRef' attribute must point to a <submodel> N N N N N N E
CompReplacedElementDeletionRef The 'comp:deletion' attribute must point to a <deletion> N N N N N N E
CompReplacedElementConvFactorRef The 'comp:conversionFactor attribute must point to a <parameter> N N N N N N E
CompReplacedElementSameReference No <replacedElement> refer to same object N N N N N N E
CompReplacedElementNoDelAndConvFact No <replacedElement> with deletion and conversionfactor N N N N N N E
CompReplacedByMustRefObject ReplacedBy must reference an object N N N N N N E
CompReplacedByMustRefOnlyOne ReplacedBy must reference only one other object. N N N N N N E
CompReplacedByAllowedAttributes Allowed attributes on <replacedBy> N N N N N N E
CompReplacedBySubModelRef The 'comp:submodelRef' attribute must point to a <submodel> N N N N N N E
CompMustReplaceSameClass Replaced classes must match. N N N N N N E
CompMustReplaceIDs Replaced IDs must be replaced with IDs. N N N N N N E
CompMustReplaceMetaIDs Replaced metaids must be replaced with metaids. N N N N N N E
CompMustReplacePackageIDs Replaced package IDs must be replaced with package IDs. N N N N N N E
CompUnresolvedReference Unresolved reference. N N N N N N E
CompNoModelInReference No model in referenced document. N N N N N N E
CompExtModDefBad Referenced <externalModelDefinitiongt; unresolvable. N N N N N N E
CompModelFlatteningFailed Model failed to flatten. N N N N N N E
CompFlatModelNotValid Flat model not valid. N N N N N N E
CompLineNumbersUnreliable Line numbers unreliable. N N N N N N W
CompFlatteningNotRecognisedReqd Flattening not implemented for required package. N N N N N N W
CompFlatteningNotRecognisedNotReqd Flattening not implemented for unrequired package. N N N N N N W
CompFlatteningNotImplementedNotReqd Flattening not implemented for unrequired package. N N N N N N W
CompFlatteningNotImplementedReqd Flattening not implemented for required package. N N N N N N W
CompFlatteningWarning Flattening reference may come from package. N N N N N N W
CompDeprecatedDeleteFunction The performDeletions functions is deprecated. N N N N N N E
CompDeprecatedReplaceFunction The performReplacementsAndConversions functions is deprecated. N N N N N N E
CompDeletedReplacement Element deleted before a subelement could be replaced. N N N N N N E
CompIdRefMayReferenceUnknownPackage The 'comp:idRef' attribute must be the 'id' of a model element N N N N N N W
CompMetaIdRefMayReferenceUnknownPkg The 'comp:metaIdRef' attribute must be the 'metaid' of a model element N N N N N N W
FbcUnknown Unknown error from fbc N N N N N N E
FbcNSUndeclared The fbc ns is not correctly declared N N N N N N E
FbcElementNotInNs Element not in fbc namespace N N N N N N E
FbcDuplicateComponentId Duplicate 'id' attribute value N N N N N N E
FbcSBMLSIdSyntax Invalid 'id' attribute N N N N N N E
FbcAttributeRequiredMissing Required fbc:required attribute on <sbml> N N N N N N E
FbcAttributeRequiredMustBeBoolean The fbc:required attribute must be Boolean N N N N N N E
FbcRequiredFalse The fbc:required attribute must be 'false' N N N N N N E
FbcOnlyOneEachListOf One of each list of allowed N N N N N N E
FbcNoEmptyListOfs ListOf elements cannot be empty N N N N N N E
FbcLOFluxBoundsAllowedElements Allowed elements on ListOfFluxBounds N N N N N N E
FbcLOObjectivesAllowedElements Allowed elements on ListOfObjectives N N N N N N E
FbcLOFluxBoundsAllowedAttributes Allowed attributes on ListOfFluxBounds N N N N N N E
FbcLOObjectivesAllowedAttributes Allowed attributes on ListOfObjectives N N N N N N E
FbcActiveObjectiveSyntax Type of activeObjective attribute N N N N N N E
FbcActiveObjectiveRefersObjective ActiveObjective must reference Objective N N N N N N E
FbcSpeciesAllowedL3Attributes Species allowed attributes N N N N N N E
FbcSpeciesChargeMustBeInteger Charge must be integer N N N N N N E
FbcSpeciesFormulaMustBeString Chemical formula must be string N N N N N N E
FbcFluxBoundAllowedL3Attributes <fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace N N N N N N E
FbcFluxBoundAllowedElements <fluxBound> may only have <notes> and <annotations> from L3 Core N N N N N N E
FbcFluxBoundRequiredAttributes Invalid attribute found on <fluxBound> object N N N N N N E
FbcFluxBoundRectionMustBeSIdRef Datatype for 'fbc:reaction' must be SIdRef N N N N N N E
FbcFluxBoundNameMustBeString The attribute 'fbc:name' must be of the data type string N N N N N N E
FbcFluxBoundOperationMustBeEnum The attribute 'fbc:operation' must be of data type FbcOperation N N N N N N E
FbcFluxBoundValueMustBeDouble The attribute 'fbc:value' must be of the data type float N N N N N N E
FbcFluxBoundReactionMustExist 'fbc:reaction' must refer to valid reaction N N N N N N E
FbcFluxBoundsForReactionConflict Conflicting set of FluxBounds for a reaction N N N N N N E
FbcObjectiveAllowedL3Attributes <objective> may only have 'metaId' and 'sboTerm' from L3 namespace N N N N N N E
FbcObjectiveAllowedElements <objective> may only have <notes> and <annotations> from L3 Core N N N N N N E
FbcObjectiveRequiredAttributes Invalid attribute found on <objective> object N N N N N N E
FbcObjectiveNameMustBeString The attribute 'fbc:name' must be of the data type string N N N N N N E
FbcObjectiveTypeMustBeEnum The attribute 'fbc:type' must be of data type FbcType. N N N N N N E
FbcObjectiveOneListOfObjectives An <objective> must have one <listOfFluxObjectives>. N N N N N N E
FbcObjectiveLOFluxObjMustNotBeEmpty <listOfFluxObjectives> subobject must not be empty N N N N N N E
FbcObjectiveLOFluxObjOnlyFluxObj Invalid element found in <listOfFluxObjectives> N N N N N N E
FbcObjectiveLOFluxObjAllowedAttribs <listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core N N N N N N E
FbcFluxObjectAllowedL3Attributes <fluxObjectivegt; may only have 'metaId' and 'sboTerm' from L3 namespace N N N N N N E
FbcFluxObjectAllowedElements <fluxObjectivegt; may only have <notes> and <annotations> from L3 Core N N N N N N E
FbcFluxObjectRequiredAttributes Invalid attribute found on <fluxObjectivegt; object N N N N N N E
FbcFluxObjectNameMustBeString The attribute 'fbc:name' must be of the data type string N N N N N N E
FbcFluxObjectReactionMustBeSIdRef Datatype for 'fbc:reaction' must be SIdRef N N N N N N E
FbcFluxObjectReactionMustExist 'fbc:reaction' must refer to valid reaction N N N N N N E
FbcFluxObjectCoefficientMustBeDouble The attribute 'fbc:coefficient' must be of the data type float N N N N N N E
LayoutUnknownError Unknown error from layout N N N N N N E
LayoutNSUndeclared The layout ns is not correctly declared N N N N N N E
LayoutElementNotInNs Element not in layout namespace N N N N N N E
LayoutDuplicateComponentId Duplicate 'id' attribute value N N N N N N E
LayoutSIdSyntax 'id' attribute incorrect syntax N N N N N N E
LayoutXsiTypeAllowedLocations 'xsi:type' allowed locations N N N N N N E
LayoutXsiTypeSyntax 'xsi:type' attribute incorrect syntax N N N N N N E
LayoutAttributeRequiredMissing Required layout:required attribute on <sbml> N N N N N N E
LayoutAttributeRequiredMustBeBoolean The layout:required attribute must be Boolean N N N N N N E
LayoutRequiredFalse The layout:required attribute must be 'false' N N N N N N E
LayoutOnlyOneLOLayouts Only one listOfLayouts on <model> N N N N N N E
LayoutLOLayoutsNotEmpty ListOf elements cannot be empty N N N N N N E
LayoutLOLayoutsAllowedElements Allowed elements on ListOfLayouts N N N N N N E
LayoutLOLayoutsAllowedAttributes Allowed attributes on ListOfLayouts N N N N N N E
LayoutLayoutAllowedElements Allowed elements on Layout N N N N N N E
LayoutLayoutAllowedCoreAttributes Allowed core attributes on Layout N N N N N N E
LayoutOnlyOneEachListOf Only one each listOf on <layout> N N N N N N E
LayoutNoEmptyListOfs ListOf elements cannot be empty N N N N N N E
LayoutLayoutAllowedAttributes <layout> must have 'id' and may have 'name' N N N N N N E
LayoutLayoutNameMustBeString 'name' must be string N N N N N N E
LayoutLOCompGlyphAllowedAttributes Attributes allowed on <listOfCompartmentGlyphs>. N N N N N N E
LayoutLOCompGlyphAllowedElements Elements allowed on <listOfCompartmentGlyphs>. N N N N N N E
LayoutLOSpeciesGlyphAllowedAttributes Attributes allowed on <listOfSpeciesGlyphs>. N N N N N N E
LayoutLOSpeciesGlyphAllowedElements Elements allowed on <listOfSpeciesGlyphs>. N N N N N N E
LayoutLORnGlyphAllowedAttributes Attributes allowed on <listOfReactionGlyphs>. N N N N N N E
LayoutLORnGlyphAllowedElements Elements allowed on <listOfReactionGlyphs>. N N N N N N E
LayoutLOAddGOAllowedAttribut Attributes allowed on <listOfAdditionalGraphicalObjectGlyphs>. N N N N N N E
LayoutLOAddGOAllowedElements Elements allowed on <listOfAdditionalGraphicalObjectGlyphs>. N N N N N N E
LayoutLayoutMustHaveDimensions Layout must have <dimensions>. N N N N N N E
LayoutLOTextGlyphAllowedAttributes Attributes allowed on <listOfTextGlyphs>. N N N N N N E
LayoutLOTextGlyphAllowedElements Elements allowed on <listOfTextGlyphs>. N N N N N N E
LayoutGOAllowedCoreElements Core elements allowed on <graphicalObject>. N N N N N N E
LayoutGOAllowedCoreAttributes Core attributes allowed on <graphicalObject>. N N N N N N E
LayoutGOAllowedElements Layout elements allowed on <graphicalObject>. N N N N N N E
LayoutGOAllowedAttributes Layout attributes allowed on <graphicalObject>. N N N N N N E
LayoutGOMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutGOMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutGOMustContainBoundingBox A <graphicalObject> must contain a <boundingBox>. N N N N N N E
LayoutCGAllowedCoreElements Core elements allowed on <compartmentGlyph>. N N N N N N E
LayoutCGAllowedCoreAttributes Core attributes allowed on <compartmentGlyph>. N N N N N N E
LayoutCGAllowedElements Layout elements allowed on <compartmentGlyph>. N N N N N N E
LayoutCGAllowedAttributes Layout attributes allowed on <compartmentGlyph>. N N N N N N E
LayoutCGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutCGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutCGCompartmentSyntax CompartmentGlyph 'compartment' must have SIdRef syntax. N N N N N N E
LayoutCGCompartmentMustRefComp CompartmentGlyph compartment must reference existing compartment. N N N N N N E
LayoutCGNoDuplicateReferences CompartmentGlyph cannot reference two objects. N N N N N N E
LayoutCGOrderMustBeDouble CompartmentGlyph order must be float. N N N N N N E
LayoutSGAllowedCoreElements Core elements allowed on <speciesGlyph>. N N N N N N E
LayoutSGAllowedCoreAttributes Core attributes allowed on <speciesGlyph>. N N N N N N E
LayoutSGAllowedElements Layout elements allowed on <speciesGlyph>. N N N N N N E
LayoutSGAllowedAttributes Layout attributes allowed on <speciesGlyph>. N N N N N N E
LayoutSGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutSGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutSGSpeciesSyntax SpeciesGlyph 'species' must have SIdRef syntax. N N N N N N E
LayoutSGSpeciesMustRefSpecies SpeciesGlyph species must reference existing species. N N N N N N E
LayoutSGNoDuplicateReferences SpeciesGlyph cannot reference two objects. N N N N N N E
LayoutRGAllowedCoreElements Core elements allowed on <reactionGlyph>. N N N N N N E
LayoutRGAllowedCoreAttributes Core attributes allowed on <reactionGlyph>. N N N N N N E
LayoutRGAllowedElements Layout elements allowed on <reactionGlyph>. N N N N N N E
LayoutRGAllowedAttributes Layout attributes allowed on <reactionGlyph>. N N N N N N E
LayoutRGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutRGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutRGReactionSyntax ReactionGlyph 'reaction' must have SIdRef syntax. N N N N N N E
LayoutRGReactionMustRefReaction ReactionGlyph reaction must reference existing reaction. N N N N N N E
LayoutRGNoDuplicateReferences ReactionGlyph cannot reference two objects. N N N N N N E
LayoutLOSpeciesRefGlyphAllowedElements Allowed elements on ListOfSpeciesReferenceGlyphs N N N N N N E
LayoutLOSpeciesRefGlyphAllowedAttribs Allowed attributes on ListOfSpeciesReferenceGlyphs N N N N N N E
LayoutLOSpeciesRefGlyphNotEmpty ListOfSpeciesReferenceGlyphs not empty N N N N N N E
LayoutGGAllowedCoreElements Core elements allowed on <generalGlyph>. N N N N N N E
LayoutGGAllowedCoreAttributes Core attributes allowed on <generalGlyph>. N N N N N N E
LayoutGGAllowedElements Layout elements allowed on <generalGlyph>. N N N N N N E
LayoutGGAllowedAttributes Layout attributes allowed on <generalGlyph>. N N N N N N E
LayoutGGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutGGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutGGReferenceSyntax GeneralGlyph 'reference' must have SIdRef syntax. N N N N N N E
LayoutGGReferenceMustRefObject GeneralGlyph 'reference' must reference existing element. N N N N N N E
LayoutGGNoDuplicateReferences GeneralGlyph cannot reference two objects. N N N N N N E
LayoutLOReferenceGlyphAllowedElements Allowed elements on ListOfReferenceGlyphs N N N N N N E
LayoutLOReferenceGlyphAllowedAttribs Allowed attributes on ListOfReferenceGlyphs N N N N N N E
LayoutLOSubGlyphAllowedElements Allowed elements on ListOfSubGlyphs N N N N N N E
LayoutLOSubGlyphAllowedAttribs Allowed attributes on ListOfSubGlyphs N N N N N N E
LayoutTGAllowedCoreElements Core elements allowed on <textGlyph>. N N N N N N E
LayoutTGAllowedCoreAttributes Core attributes allowed on <textGlyph>. N N N N N N E
LayoutTGAllowedElements Layout elements allowed on <textGlyph>. N N N N N N E
LayoutTGAllowedAttributes Layout attributes allowed on <textGlyph>. N N N N N N E
LayoutTGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutTGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutTGOriginOfTextSyntax TextGlyph 'originOfText' must have SIdRef syntax. N N N N N N E
LayoutTGOriginOfTextMustRefObject TextGlyph 'originOfText' must reference existing element. N N N N N N E
LayoutTGNoDuplicateReferences TextGlyph cannot reference two objects. N N N N N N E
LayoutTGGraphicalObjectSyntax TextGlyph 'graphicalObject' must have SIdRef syntax. N N N N N N E
LayoutTGGraphicalObjectMustRefObject TextGlyph 'graphicalObject' must reference existing element. N N N N N N E
LayoutTGTextMustBeString TextGlyph 'text' must be string. N N N N N N E
LayoutSRGAllowedCoreElements Core elements allowed on <speciesReferenceGlyphgt;. N N N N N N E
LayoutSRGAllowedCoreAttributes Core attributes allowed on <speciesReferenceGlyphgt;. N N N N N N E
LayoutSRGAllowedElements Layout elements allowed on <speciesReferenceGlyphgt;. N N N N N N E
LayoutSRGAllowedAttributes Layout attributes allowed on <speciesReferenceGlyphgt;. N N N N N N E
LayoutSRGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutSRGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutSRGSpeciesReferenceSyntax SpeciesReferenceGlyph 'speciesReference' must have SIdRef syntax. N N N N N N E
LayoutSRGSpeciesRefMustRefObject SpeciesReferenceGlyph 'speciesReference' must reference existing element. N N N N N N E
LayoutSRGNoDuplicateReferences SpeciesReferenceGlyph cannot reference two objects. N N N N N N E
LayoutSRGSpeciesGlyphSyntax SpeciesReferenceGlyph 'speciesGlyph' must have SIdRef syntax. N N N N N N E
LayoutSRGSpeciesGlyphMustRefObject SpeciesReferenceGlyph 'speciesGlyph' must reference existing element. N N N N N N E
LayoutSRGRoleSyntax SpeciesReferenceGlyph 'role' must be string from enumeration. N N N N N N E
LayoutREFGAllowedCoreElements Core elements allowed on <referenceGlyph>. N N N N N N E
LayoutREFGAllowedCoreAttributes Core attributes allowed on <referenceGlyph>. N N N N N N E
LayoutREFGAllowedElements Layout elements allowed on <referenceGlyph>. N N N N N N E
LayoutREFGAllowedAttributes Layout attributes allowed on <referenceGlyph>. N N N N N N E
LayoutREFGMetaIdRefMustBeIDREF Layout 'metIdRef' must be IDREF. N N N N N N E
LayoutREFGMetaIdRefMustReferenceObject Layout 'metIdRef' must reference existing object. N N N N N N E
LayoutREFGReferenceSyntax ReferenceGlyph 'reference' must have SIdRef syntax. N N N N N N E
LayoutREFGReferenceMustRefObject ReferenceGlyph 'reference' must reference existing element. N N N N N N E
LayoutREFGNoDuplicateReferences ReferenceGlyph cannot reference two objects. N N N N N N E
LayoutREFGGlyphSyntax ReferenceGlyph 'glyph' must have SIdRef syntax. N N N N N N E
LayoutREFGGlyphMustRefObject ReferenceGlyph 'glyph' must reference existing element. N N N N N N E
LayoutREFGRoleSyntax ReferenceGlyph 'role' must be string. N N N N N N E
LayoutPointAllowedCoreElements Core elements allowed on <point>. N N N N N N E
LayoutPointAllowedCoreAttributes Core attributes allowed on <point>. N N N N N N E
LayoutPointAllowedAttributes Layout attributes allowed on <point>. N N N N N N E
LayoutPointAttributesMustBeDouble Layout 'x', 'y' and 'z' must be float. N N N N N N E
LayoutBBoxAllowedCoreElements Core elements allowed on <boundingBox>. N N N N N N E
LayoutBBoxAllowedCoreAttributes Core attributes allowed on <boundingBox>. N N N N N N E
LayoutBBoxAllowedElements Layout elements allowed on <boundingBox>. N N N N N N E
LayoutBBoxAllowedAttributes Layout attributes allowed on <boundingBox>. N N N N N N E
LayoutBBoxConsistent3DDefinition Layout consistent dimensions on a <boundingBox> N N N N N N E
LayoutCurveAllowedCoreElements Core elements allowed on <curve>. N N N N N N E
LayoutCurveAllowedCoreAttributes Core attributes allowed on <curve>. N N N N N N E
LayoutCurveAllowedElements Layout elements allowed on <curve>. N N N N N N E
LayoutCurveAllowedAttributes Layout attributes allowed on <curve>. N N N N N N E
LayoutLOCurveSegsAllowedAttributes Allowed attributes on ListOfCurveSegments N N N N N N E
LayoutLOCurveSegsAllowedElements Allowed elements on ListOfCurveSegments N N N N N N E
LayoutLOCurveSegsNotEmpty No empty ListOfCurveSegments N N N N N N E
LayoutLSegAllowedCoreElements Core elements allowed on <lineSegment>. N N N N N N E
LayoutLSegAllowedCoreAttributes Core attributes allowed on <lineSegment>. N N N N N N E
LayoutLSegAllowedElements Layout elements allowed on <lineSegment>. N N N N N N E
LayoutLSegAllowedAttributes Layout attributes allowed on <lineSegment>. N N N N N N E
LayoutCBezAllowedCoreElements Core elements allowed on <cubicBezier>. N N N N N N E
LayoutCBezAllowedCoreAttributes Core attributes allowed on <cubicBezier>. N N N N N N E
LayoutCBezAllowedElements Layout elements allowed on <cubicBezier>. N N N N N N E
LayoutCBezAllowedAttributes Layout attributes allowed on <cubicBezier>. N N N N N N E
LayoutDimsAllowedCoreElements Core elements allowed on <dimensions>. N N N N N N E
LayoutDimsAllowedCoreAttributes Core attributes allowed on <dimensions>. N N N N N N E
LayoutDimsAllowedAttributes Layout attributes allowed on <dimensions>. N N N N N N E
LayoutDimsAttributesMustBeDouble Layout 'width', 'height' and 'depth' must be float. N N N N N N E
QualUnknown Unknown error from qual. N N N N N N E
QualNSUndeclared The qual ns is not correctly declared. N N N N N N E
QualElementNotInNs Element not in qual namespace. N N N N N N E
QualFunctionTermBool FunctionTerm should return boolean. N N N N N N W
QualMathCSymbolDisallowed CSymbol time or delay not allowed. N N N N N N W
QualDuplicateComponentId Duplicate 'id' attribute value. N N N N N N E
QualAttributeRequiredMissing Required qual:required attribute on <sbml>. N N N N N N E
QualAttributeRequiredMustBeBoolean The qual:required attribute must be Boolean. N N N N N N E
QualRequiredTrueIfTransitions The qual:required attribute must be 'true' if math changes. N N N N N N E
QualOneListOfTransOrQS Only one <listOfTransitions> or <listOfQualitativeSpeciesgt; allowed. N N N N N N E
QualEmptyLONotAllowed Empty <listOfTransitions> or <listOfQualitativeSpeciesgt; not allowed. N N N N N N E
QualLOTransitiondAllowedElements Elements allowed on <listOfTransitions>. N N N N N N E
QualLOQualSpeciesAllowedElements Elements allowed on <listOfTransitions>. N N N N N N E
QualLOQualSpeciesAllowedAttributes Attributes allowed on <listOfQualitativeSpeciesgt;. N N N N N N E
QualLOTransitionsAllowedAttributes Attributes allowed on <listOfTransitions>. N N N N N N E
QualQualSpeciesAllowedCoreAttributes Core attributes allowed on <qualitativeSpeciesgt;. N N N N N N E
QualQualSpeciesAllowedElements Elements allowed on <qualitativeSpeciesgt;. N N N N N N E
QualQualSpeciesAllowedAttributes Attributes allowed on <qualitativeSpeciesgt;. N N N N N N E
QualConstantMustBeBool Attribute 'constant' on <qualitativeSpeciesgt; must be boolean. N N N N N N E
QualNameMustBeString Attribute 'name' on <qualitativeSpeciesgt; must be string. N N N N N N E
QualInitialLevelMustBeInt Attribute 'initialLevel' on <qualitativeSpeciesgt; must be integer. N N N N N N E
QualMaxLevelMustBeInt Attribute 'maxLevel' on <qualitativeSpeciesgt; must be integer. N N N N N N E
QualCompartmentMustReferExisting Attribute 'compartment' on <qualitativeSpeciesgt; must reference compartment. N N N N N N E
QualInitialLevelCannotExceedMax Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot exceed maxLevel. N N N N N N E
QualConstantQSCannotBeOutput Constant <qualitativeSpeciesgt; cannot be an Output. N N N N N N E
QualQSAssignedOnlyOnce A <qualitativeSpeciesgt; can only be assigned once. N N N N N N E
QualInitalLevelNotNegative Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot be negative. N N N N N N E
QualMaxLevelNotNegative Attribute 'maxLevel' on <qualitativeSpeciesgt; cannot be negative. N N N N N N E
QualTransitionAllowedCoreAttributes Core attributes allowed on <transition>. N N N N N N E
QualTransitionAllowedElements Elements allowed on <transition>. N N N N N N E
QualTransitionAllowedAttributes Attributes allowed on <transition>. N N N N N N E
QualTransitionNameMustBeString Attribute 'name' on <transition> must be string. N N N N N N E
QualTransitionLOElements ListOf elements on <transition>. N N N N N N E
QualTransitionEmptyLOElements ListOf elements on <transition> not empty. N N N N N N E
QualTransitionLOInputElements Elements on <listOfInputs>. N N N N N N E
QualTransitionLOOutputElements Elements on <listOfOutputs>. N N N N N N E
QualTransitionLOFuncTermElements Elements on <listOfFunctionTerms>. N N N N N N E
QualTransitionLOInputAttributes Attributes allowed on <listOfInputs>. N N N N N N E
QualTransitionLOOutputAttributes Attributes allowed on <listOfOutputs>. N N N N N N E
QualTransitionLOFuncTermAttributes Attributes allowed on <listOfFunctionTerms>. N N N N N N E
QualTransitionLOFuncTermExceedMax <listOfFunctionTerms> cannot make qualitativeSpecies exceed maxLevel. N N N N N N E
QualTransitionLOFuncTermNegative <listOfFunctionTerms> cannot make qualitativeSpecies negative. N N N N N N E
QualInputAllowedCoreAttributes Core attributes allowed on <input>. N N N N N N E
QualInputAllowedElements Elements allowed on <input>. N N N N N N E
QualInputAllowedAttributes Attributes allowed on <input>. N N N N N N E
QualInputNameMustBeString Attribute 'name' on <input> must be string. N N N N N N E
QualInputSignMustBeSignEnum Attribute 'sign' on <input> must be enum. N N N N N N E
QualInputTransEffectMustBeInputEffect Attribute 'transitionEffect' on <input> must be enum. N N N N N N E
QualInputThreshMustBeInteger Attribute 'thresholdLevel' on <input> must be non negative integer. N N N N N N E
QualInputQSMustBeExistingQS Attribute 'qualitativeSpecies' on <input> must refer to existing. N N N N N N E
QualInputConstantCannotBeConsumed Constant <input> cannot be consumed. N N N N N N E
QualInputThreshMustBeNonNegative Attribute 'thresholdLevel' on <input> must be non negative integer. N N N N N N E
QualOutputAllowedCoreAttributes Core attributes allowed on <output>. N N N N N N E
QualOutputAllowedElements Elements allowed on <output>. N N N N N N E
QualOutputAllowedAttributes Attributes allowed on <output>. N N N N N N E
QualOutputNameMustBeString Attribute 'name' on <output> must be string. N N N N N N E
QualOutputTransEffectMustBeOutput Attribute 'transitionEffect' on <output> must be enum. N N N N N N E
QualOutputLevelMustBeInteger Attribute 'outputLevel' on <output> must be non negative integer. N N N N N N E
QualOutputQSMustBeExistingQS Attribute 'qualitativeSpecies' on <output> must refer to existing. N N N N N N E
QualOutputConstantMustBeFalse Constant 'qualitativeSpecies' cannot be <output>. N N N N N N E
QualOutputProductionMustHaveLevel <output> being produced must have level. N N N N N N E
QualOutputLevelMustBeNonNegative Attribute 'outputLevel' on <output> must be non negative integer. N N N N N N E
QualDefaultTermAllowedCoreAttributes Core attributes allowed on <defaultTerm>. N N N N N N E
QualDefaultTermAllowedElements Elements allowed on <defaultTerm>. N N N N N N E
QualDefaultTermAllowedAttributes Attributes allowed on <defaultTerm>. N N N N N N E
QualDefaultTermResultMustBeInteger Attribute 'resultLevel' on <defaultTerm> must be non negative integer. N N N N N N E
QualDefaultTermResultMustBeNonNeg Attribute 'resultLevel' on <defaultTerm> must be non negative integer. N N N N N N E
QualFuncTermAllowedCoreAttributes Core attributes allowed on <functionTerm>. N N N N N N E
QualFuncTermAllowedElements Elements allowed on <functionTerm>. N N N N N N E
QualFuncTermAllowedAttributes Attributes allowed on <functionTerm>. N N N N N N E
QualFuncTermOnlyOneMath Only one <math> on <functionTerm>. N N N N N N E
QualFuncTermResultMustBeInteger Attribute 'resultLevel' on <functionTerm> must be non negative integer. N N N N N N E
QualFuncTermResultMustBeNonNeg Attribute 'resultLevel' on <functionTerm> must be non negative integer.. N N N N N N E

Category codes associated with SBMLError objects

As discussed above, each SBMLError object contains a value for a category identifier, describing the type of issue that the SBMLError object represents. The category can be retrieved from an SBMLError object using the method SBMLError.getCategory(). The following table lists each possible value and a brief description of its meaning.

As is the case with the error codes, in the libSBML Python language interface, the category identifiers are currently implemented as static integer constants defined in the interface class libsbml.

The following table lists each possible value and a brief description of its meaning.

Enumerator Meaning
LIBSBML_CAT_SBMLGeneral error not falling into another category below.
LIBSBML_CAT_SBML_L1_COMPATCategory of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model from SBML Level 2 to SBML Level 1.
LIBSBML_CAT_SBML_L2V1_COMPATCategory of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 1.
LIBSBML_CAT_SBML_L2V2_COMPATCategory of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 2.
LIBSBML_CAT_GENERAL_CONSISTENCYCategory of errors that can occur while validating general SBML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_IDENTIFIER_CONSISTENCYCategory of errors that can occur while validating symbol identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_UNITS_CONSISTENCYCategory of errors that can occur while validating the units of measurement on quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_MATHML_CONSISTENCYCategory of errors that can occur while validating MathML formulas in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_SBO_CONSISTENCYCategory of errors that can occur while validating SBO identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_OVERDETERMINED_MODELError in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2–4 and Level 3 Version 1 specifications.
LIBSBML_CAT_SBML_L2V3_COMPATCategory of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 3.
LIBSBML_CAT_MODELING_PRACTICECategory of warnings about recommended good practices involving SBML and computational modeling. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)
LIBSBML_CAT_INTERNAL_CONSISTENCYCategory of errors that can occur while validating libSBML's internal representation of SBML constructs. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)
LIBSBML_CAT_SBML_L2V4_COMPATCategory of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 4.
LIBSBML_CAT_SBML_L3V1_COMPAT

Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1.

Severity codes associated with SBMLError objects

In libSBML version 5.10.0 there are no additional severity codes beyond those defined by XMLError. They are implemented as static integer constants defined in the interface class libsbml, and have names beginning with LIBSBML_SEV_.

Public Member Functions

def getCategory
 
def getCategoryAsString
 
def getColumn
 
def getErrorId
 
def getErrorIdOffset
 
def getLine
 
def getMessage
 
def getPackage
 
def getSeverity
 
def getSeverityAsString
 
def getShortMessage
 
def getStandardMessage
 
def isError
 
def isFatal
 
def isInfo
 
def isInternal
 
def isSystem
 
def isValid
 
def isWarning
 
def isXML
 
def setColumn
 
def setLine
 

Member Function Documentation

def libsbml.XMLError.getCategory (   self)
inherited

Python method signature(s):

getCategory(XMLError self)   long

Returns the category of this error.

XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.

Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.

Returns
the category of this XMLError.
See also
getSeverity()
getCategoryAsString()
def libsbml.XMLError.getCategoryAsString (   self)
inherited

Python method signature(s):

getCategoryAsString(XMLError self)   string

Returns a string describing the category of this error.

XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.

Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.

Returns
string representing the category of this XMLError.
See also
getCategory()
getSeverityAsString()
def libsbml.XMLError.getColumn (   self)
inherited

Python method signature(s):

getColumn(XMLError self)   long

Returns the column number in the XML input near where the error, warning or other diagnostic occurred.

We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Returns
the column number
See also
getLine()
def libsbml.XMLError.getErrorId (   self)
inherited

{core}

Representation of errors, warnings and other diagnostics

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

LibSBML can be configured to use any of a number of XML parsers; at the time of this writing, libSBML supports Xerces versions 2.4 through 3.1, Expat version 1.95.x and higher, and libxml2 version 2.6.16 and higher. These parsers each report different status codes for the various exceptions that can occur during XML processing. The XMLError object class abstracts away from the particular diagnostics reported by the different parsers and presents a single uniform interface and set of status codes, along with operations for manipulating the error objects.

When the libSBML XML parser layer encounters an error in the XML content being processed, or when there is something else wrong (such as an out-of-memory condition), the problems are reported as XMLError objects. Each XMLError object instance has an identification number that identifies the nature of the problem. This error identifier is one of the constants listed in the next section below. Applications can use the error identifiers as a means of recognizing the error encountered and changing their behavior if desired.

Integer error codes are useful for software, but not so much for telling humans what happened. For this reason, XMLError also provides two text messages describing the nature of the error. These messages are accessible by means of the methods XMLError.getShortMessage() and XMLError.getMessage(). The method XMLError.getShortMessage() returns a very brief synopsis of the warning or error condition, whereas XMLError.getMessage() returns a longer explanation. These text strings are suitable for displaying to human users.

Each XMLError object also contains a category code; its value may be retrieved using the method XMLError.getCategory(). Category values are drawn from a set of constants whose names begin with the characters LIBSBML_CAT_, described below.  Categories are used by libSBML to provide more information to calling programs about the nature of a given error.

In addition to category codes, each XMLError object also has a severity code; its value may be retrieved using the method XMLError.getSeverity(). Severity code values are drawn from a set of constants whose names begin with the characters LIBSBML_SEV_, described below. Severity levels range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL).

Finally, XMLError objects record the line and column near where the problem occurred in the XML content. The values can be retrieved using the methods XMLError.getLine() and XMLError.getColumn(). We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Possible XMLError error codes. Depending on the programming language in use, the Enumerator values will be defined either as a value from the enumeration long or as integer constants. To make this table more compact, we have shortened the identifiers for the category and severity codes to their essential parts. To get the actual names of the constants, prepend LIBSBML_CAT_ to the category names and LIBSBML_SEV_ to the severity names shown in the two right-hand columns.
Enumerator Meaning Category Severity
XMLUnknownErrorUnrecognized error encountered internallyINTERNALFATAL
XMLOutOfMemory Out of memorySYSTEMFATAL
XMLFileUnreadable File unreadableSYSTEMERROR
XMLFileUnwritable File unwritableSYSTEMERROR
XMLFileOperationErrorError encountered while attempting file operationSYSTEMERROR
XMLNetworkAccessErrorNetwork access errorSYSTEMERROR
InternalXMLParserErrorInternal XML parser state errorINTERNALFATAL
UnrecognizedXMLParserCodeXML parser returned an unrecognized error codeINTERNALFATAL
XMLTranscoderErrorCharacter transcoder errorINTERNALFATAL
MissingXMLDeclMissing XML declaration at beginning of XML inputXMLERROR
MissingXMLEncodingMissing encoding attribute in XML declarationXMLERROR
BadXMLDeclInvalid or unrecognized XML declaration or XML encodingXMLERROR
BadXMLDOCTYPEInvalid, malformed or unrecognized XML DOCTYPE declarationXMLERROR
InvalidCharInXMLInvalid character in XML contentXMLERROR
BadlyFormedXMLXML content is not well-formedXMLERROR
UnclosedXMLTokenUnclosed XML tokenXMLERROR
InvalidXMLConstructXML construct is invalid or not permittedXMLERROR
XMLTagMismatchElement tag mismatch or missing tagXMLERROR
DuplicateXMLAttributeDuplicate XML attributeXMLERROR
UndefinedXMLEntityUndefined XML entityXMLERROR
BadProcessingInstructionInvalid, malformed or unrecognized XML processing instructionXMLERROR
BadXMLPrefixInvalid or undefined XML namespace prefixXMLERROR
BadXMLPrefixValueInvalid XML namespace prefix valueXMLERROR
MissingXMLRequiredAttributeMissing a required XML attributeXMLERROR
XMLAttributeTypeMismatchData type mismatch for the value of an attributeXMLERROR
XMLBadUTF8ContentInvalid UTF8 contentXMLERROR
MissingXMLAttributeValueMissing or improperly formed attribute valueXMLERROR
BadXMLAttributeValueInvalid or unrecognizable attribute valueXMLERROR
BadXMLAttributeInvalid, unrecognized or malformed attributeXMLERROR
UnrecognizedXMLElementElement either not recognized or not permittedXMLERROR
BadXMLCommentBadly formed XML commentXMLERROR
BadXMLDeclLocationXML declaration not permitted in this locationXMLERROR
XMLUnexpectedEOFReached end of input unexpectedlyXMLERROR
BadXMLIDValueValue is invalid for XML ID, or has already been usedXMLERROR
BadXMLIDRefXML ID value was never declaredXMLERROR
UninterpretableXMLContentUnable to interpret contentXMLERROR
BadXMLDocumentStructureBad XML document structureXMLERROR
InvalidAfterXMLContentEncountered invalid content after expected contentXMLERROR
XMLExpectedQuotedStringExpected to find a quoted stringXMLERROR
XMLEmptyValueNotPermittedAn empty value is not permitted in this contextXMLERROR
XMLBadNumberInvalid or unrecognized numberXMLERROR
XMLBadColonColon characters are invalid in this contextXMLERROR
MissingXMLElementsOne or more expected elements are missingXMLERROR
XMLContentEmptyMain XML content is emptyXMLERROR
Enumerator Meaning
LIBSBML_CAT_INTERNAL A problem involving the libSBML software itself or the underlying XML parser. This almost certainly indicates a software defect (i.e., bug) in libSBML. Please report instances of this to the libSBML developers.
LIBSBML_CAT_SYSTEM A problem reported by the operating system, such as an inability to read or write a file. This indicates something that is not a program error but is outside of the control of libSBML.
LIBSBML_CAT_XML A problem in the XML content itself. This usually arises from malformed XML or the use of constructs not permitted in SBML.
Enumerator Meaning
LIBSBML_SEV_INFO The error is actually informational and not necessarily a serious problem.
LIBSBML_SEV_WARNING The error object represents a problem that is not serious enough to necessarily stop the problem, but applications should take note of the problem and evaluate what its implications may be.
LIBSBML_SEV_ERROR The error object represents a serious error. The application may continue running but it is unlikely to be able to continue processing the same XML file or data stream.
LIBSBML_SEV_FATAL A serious error occurred, such as an out-of-memory condition, and the software should terminate immediately.

Python method signature(s):

getErrorId(XMLError self)   long

Returns the identifier of this error.

Returns
the error code for this error.
See also
getMessage()
getShortMessage()
getCategory()
getSeverity()
def libsbml.XMLError.getErrorIdOffset (   self)
inherited

Python method signature(s):

getErrorIdOffset(XMLError self)   long

Returns libSBML's internal numerical offset for the error code associated with this error.

In the SBML Level 3 package specifications, package validation rules are identified by 5-digit numbers prefixed with the nickname of the package itself—e.g., “comp-10101”, “fbc-20301”, etc. Historically, libSBML reported error codes as pure integers, and some application software systems make decisions based on the numerical values of the error codes. To permit these applications to continue to function in this fashion, libSBML internally continues to maintain error identifiers as pure integers. To handle the possibility that errors may come from package extensions, libSBML uses numerical offsets added to the internal error codes. These offsets add two leading digits to the regular 5-digit error codes; for example, “comp” error codes are stored as 1010101, 1020102, etc. The offset in this case is 1000000. Another package will have the offset 2000000, yet another will have 3000000, etc.

This method returns the integer offset in this error's error code. Calling applications can get the 5-digit package-specific number for a given error code by subtracting the offset from the value reported by getErrorId():

 getErrorId() - getErrorIdOffset()

When libSBML produces error messages, it combines the text string returned by getPackage() with the subtracted value of the error code, to produce a text string of the form “comp-10101”.

See also
getErrorId()
getPackage()
def libsbml.XMLError.getLine (   self)
inherited

Python method signature(s):

getLine(XMLError self)   long

Returns the line number in the XML input near where the error, warning or other diagnostic occurred.

We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0 or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.

Returns
the line number
See also
getColumn()
def libsbml.XMLError.getMessage (   self)
inherited

Python method signature(s):

getMessage(XMLError self)   string

Returns the message text of this error.

The message associated with an error object describes the nature of the problem. The message returned by this method is generally longer and clearer than the message returned by XMLError.getShortMessage(), but not in all cases.

Callers may use XMLError.getCategory() and XMLError.getSeverity() to obtain additional information about the nature and severity of the problem.

Returns
the message text
See also
getErrorId()
getShortMessage()
getCategory()
getSeverity()
def libsbml.XMLError.getPackage (   self)
inherited

Python method signature(s):

getPackage(XMLError self)   string

Returns the SBML Level 3 package extension (if any) that logged this error.

Each error logged by an libSBML extension for SBML Level 3 packages includes a record of the package that logged it. The field is a simple text string. If the string is empty or has the value 'core', then the error came from libSBML core; otherwise, the string will be the short-form name of the package (e.g., 'comp' for the Hierarchical Model Composition package).

Returns
a string representing the name of the package that logged this error. If the error did not come from a package extension, the value will be the empty string or 'core'.
def libsbml.XMLError.getSeverity (   self)
inherited

Python method signature(s):

getSeverity(XMLError self)   long

Returns the severity of this error.

XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.

Returns
the severity of this XMLError.
See also
getSeverityAsString()
getCategory()
def libsbml.XMLError.getSeverityAsString (   self)
inherited

Python method signature(s):

getSeverityAsString(XMLError self)   string

Returns a string describing the severity level of this error.

XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.

Returns
string representing the severity of this XMLError.
See also
getSeverity()
getCategoryAsString()
def libsbml.XMLError.getShortMessage (   self)
inherited

Python method signature(s):

getShortMessage(XMLError self)   string

Returns a brief message for this error.

This is an alternative error message that, in general, is as short as the authors could make it. However, brevity is often inversely proportional to clarity, so this short message may not be sufficiently informative to understand the nature of the error. Calling applications may wish to check XMLError.getMessage() in addition or instead.

Returns
the short error message text
See also
getErrorId()
getMessage()
getCategory()
getSeverity()
def libsbml.XMLError.getStandardMessage (   args)
inherited

Python method signature(s):

getStandardMessage(int code)   string

Returns a copy of the message string associated with the given predefined XMLError code.

Parameters
codethe error code whose message is sought; it must be a predefined value from the set of predefined error identifiers.
def libsbml.XMLError.isError (   self)
inherited

Python method signature(s):

isError(XMLError self)   bool

Predicate returning True or False depending on whether this error is a significant error.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_ERROR from the set of predefined severity codes.

Returns
True if this error is an error, False otherwise.
See also
isInfo()
isWarning()
isFatal()
def libsbml.XMLError.isFatal (   self)
inherited

Python method signature(s):

isFatal(XMLError self)   bool

Predicate returning True or False depending on whether this error is a fatal run-time error.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_FATAL from the set of predefined severity codes.

Returns
True if this error is a fatal error, False otherwise.
See also
isInfo()
isWarning()
isError()
def libsbml.XMLError.isInfo (   self)
inherited

Python method signature(s):

isInfo(XMLError self)   bool

Predicate returning True or False depending on whether this error object is for information purposes only.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_INFO from the set of predefined severity codes.

Returns
True if this XMLError is for informational purposes only, False otherwise.
See also
isWarning()
isError()
isFatal()
def libsbml.XMLError.isInternal (   self)
inherited

Python method signature(s):

isInternal(XMLError self)   bool

Predicate returning True or False depending on whether this error resulted from an internal program error.

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_INTERNAL from the set of predefined category codes.

Returns
True or False
See also
isSystem()
isXML()
def libsbml.XMLError.isSystem (   self)
inherited

Python method signature(s):

isSystem(XMLError self)   bool

Predicate returning True or False depending on whether this error was generated by the operating system.

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_SYSTEM from the set of predefined category codes.

Returns
True or False
See also
isInternal()
isXML()
def libsbml.XMLError.isValid (   self)
inherited

Python method signature(s):

isValid(XMLError self)   bool

Predicate returning True or False depending on whether this error resulted from a problem or whether it was logged as an unknown error.

This is equivalent to obtaining the error identifier from an XMLError object (via XMLError.getErrorId()) and then comparing it to the value XMLUnknownError or UnknownError from the set of predefined error codes.

Returns
True or False
def libsbml.XMLError.isWarning (   self)
inherited

Python method signature(s):

isWarning(XMLError self)   bool

Predicate returning True or False depending on whether this error object is a warning.

This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_WARNING from the set of predefined severity codes.

Returns
True if this error is a warning, False otherwise.
See also
isInfo()
isError()
isFatal()
def libsbml.XMLError.isXML (   self)
inherited

Python method signature(s):

isXML(XMLError self)   bool

Predicate returning True or False depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).

This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_XML from the set of predefined category codes.

Returns
True or False
See also
isInternal()
isSystem()
def libsbml.XMLError.setColumn (   self,
  args 
)
inherited

Python method signature(s):

setColumn(XMLError self, long column)   int

Sets the column number where this error occurred.

Parameters
columna long integer, the column number to set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setLine()
def libsbml.XMLError.setLine (   self,
  args 
)
inherited

Python method signature(s):

setLine(XMLError self, long line)   int

Sets the line number where this error occurred.

Parameters
linea long integer, the line number to set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setColumn()